Protocol demonstrates effective RNA detection in FFPE human brain tissue, suggesting methods to avoid sectioning artifacts and maintain morphology.
The Xenium In Situ Gene Expression platform from 10x Genomics enables high-plex, targeted RNA detection at subcellular resolution, supporting spatially resolved cell typing and molecular profiling. While an optimized tissue preparation protocol was provided by 10x, formalin-fixed paraffin-embedded (FFPE) post-mortem human brain tissue presents unique challenges due to its high lipid content. Organic solvents used during paraffin embedding extract lipids from myelin-rich white matter, leading to membrane disruption and sectioning artifacts such as compression, chatter, and fragmentation. In addition, the Xenium platform provides slides with a special coating and a defined 10.45 mm × 22.45 mm capture area, which demand precise handling during tissue placement to maximize the utilization of the capture area and ensure tissue quality. In this protocol, we demonstrate the procedure for attaching three 6 mm × 8 mm sections of human brain tissue. This protocol outlines a standardized workflow with quality control checkpoints and troubleshooting to preserve morphology, minimize artifacts, and ensure reproducibility for high quality Xenium assays on FFPE human brain tissue.
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Cao et al. (2025) studied this question.
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